Yes, I'm using Gen 3 suite to allow the pokemon to level up via evolution stone w/ the new stone in question. The game recognizes that its an evolution stone. It shows the correct graphic on the stone, correct description. It allows me to use it on said pokemon. When I use it, various things happen. I haven't had a successful clean evolution from it. Usually it WILL work, but it will boost my pokemon to a random level, or if (I'm assuming) the level is too high, it causes the game to loop and more or less freeze. (I'm using Fire Red btw)
For testing purposes, I too used this program to see how user-friendly it was... Extremely user friendly, by the way, so props to you... However, I also encounter this level-change effect. I turned the blank Item Slot beneath the Leaf Stone into a Dawn Stone. Before I was going to implement it, though, I had to test to see if the stone would evolve a Pokemon or cause some sort of glitch.
The effect it had I did not expect.
This is the order of events:
1) Created Dawn Stone.
2) Registered Bulbasaur to have a split evolution to evolve into Vee, Pokemon #387. (Don't ask, this was just for testing purposes)
3) Created an event to give me the National Dex as well as the Dawn Stone so that Bulbasaur could actually perform evolution.
4) Proceeded to open the Rom to test.
5) Activated the script.
6) Received the Dawn Stone and National Dex.
7) Realized the guy was giving away infinite free Dawn Stones.
8) Made a note to fix that.
9) Took a hundred free Dawn Stones because why not?
10) Opened my bag and clicked on the Dawn Stone to use it.
11) Selected my Lv. 6 Bulbasaur.
12) Bulbasaur evolved successfully into Vee.
13) Checked Vee's Level.
14) Vee was Lv. 4.
15) Restarted the Rom
16) Repeated from step 5
17) Same results
18) Repeated from step 5 again.
19) Same results.
20) Restarted the Rom
21) Leveled up Bulbasaur to Lv. 7 before evolving again.
22) Evolved Bulbasaur.
23) Vee was Level 5.
24) Repeated from step 20.
25) Same Results.
26) Restarted the Rom.
27) Leveled Bulbasaur up to Level 8.
28) Evolved into Vee.
29) Checked Vee's Level... Level 6.
30) Proceeded to write this in-depth 30 step process list for your viewing displeasure.
It should be noted that I am using the "Gen III Hacking Suite"... AKA "The Lord of the Tools". Also, Day&Night has been implemented on my rom. My map editor atm is A-Map, until ShinyQuagsire finishes the Map Editor of Happiness, or MEH. And my script editor is PKSVUI. My Emulator is VisualBoy Advance. I have yet to proceed to use an image editor due to hoping one of the tools I am presently using will implement a full-function image editor into their system. (If that point doesn't come, then I will be using Overworld Editor Rebirth.) The lack of image-editor is noted just for completeness.
EDIT: Oh, by the way, if at any point you figure out what is changing the levels of our Pokemon, Let me know. I want to implement a script that forces all of the player's Pokemon to become a lower Level if they are at a certain Level or above. (i.e. make a permanent change to all Pokemon over Level 50, making them become Level 50.) This script is going to be used for preventing a player from having a team of Level 100 Pokemon and just clearing event after event with no trouble.
EDIT: I feel it should be obvious, but just in case, the events I'm referencing are post-game events.